Homographs

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Some words look identical except that the stress is on a different syllable:

בואי, קומי, שירי, שובי etc. – When the the accent is on the first syllable, these are feminine imperatives ("come"); when the accent is on the final syllable they are possessive nouns ("my coming")
באה, קמה, שרה, שבה etc. – These verbs can be either past tense (when the final syllable is stressed) or present tense (when the first syllable is stressed).
בנו – When the first syllable of the word is stressed, this means "in us"; when the last syllable is stressed, it is the plural past tense of the root "בנה" (they built). See, though, Yechezkel 27:5 where the stress is pushed back a syllable (נסוג אחור), so that it looks like it should mean "in us" while it actually means "they built".
שבו – When the accent is on the first syllable the verb means "they returned, from the root "שוב"; when it is on the last syllable it means "they took captive", from the root "שבה", to take captive.

Some words are indistinguishable except for the fact that there is a mappik in one of their letters:

אִשָּׁה (woman) vs אִישָׁהּ (her husband) – See Bemidbar 5:29.
השקה (gave to drink) vs. הִשְׁקָהּ (give her to drink) – Compare Bemidbar 5:24 and 27.

The word "עֲרוּמִּים" (masculine, plural of naked) looks almost identical to "עֲרוּמִים" (masculine, plural of crafty), except that the first word has a dagesh in the "מ".
The word "חַטָּאִים" (sinners) looks almost identical to "חֲטָאִים" (sins) except for the dagesh in the "ט" (and the chataf vs. chataf patach under the "ח").

See Bavli Berakhot 10a regarding Tehillim 104:5 "יִתַּמּוּ חַטָּאִים מִן הָאָרֶץ וּרְשָׁעִים עוֹד אֵינָם ". Though the simple sense of the verse is that "sinners should cease from the earth and the wicked will be no more", the Bavli makes a homily through a play on the word "חֲטָאִים" that sins should cease, and then by default there will be no more wicked.

The word "אֲמָתָהּ" (her maidservant) is similar to "אַמָּתָהּ" (her cubit), except for the dagesh in the "מ" (and the chataf vs. chataf patach under the "א").

See Shemot 2:5 where Paroh's daughter sends her "אָמָה" to fetch Moshe's basket. Shemot Rabbah suggests that she stretched forth "her hand (cubit)", but Rashi argues that if so, the word should have had a dagesh in the "מ". Without a dagesh in the word, the verse means that Paroh's daughter sent forth "her maidservant".

The word יַמִּים with a dagesh means sea, while "יַמִם" without a dagesh is a type of animal.

Some words look identical except that one has a regular vowel and the other has a chataf in its place.

חַטָּאִים / חֲטָאִים – The word "חַטָּאִים" means sinner (the singular form of the word being "חַטָּא"), while "חֲטָאִים" means sins (with the singular form being "חֵטְא"). [A second difference between the words is the presence/absence of a dagesh in the "ט"; see above]

"אֲמָתָהּ" / "אַמָּתָהּ" – The word "אֲמָתָהּ" (her maidservant) is similar to "אַמָּתָהּ" (her cubit) except for the chataf vs. chataf patach under the "א" (and the dagesh in the "מ").

אור – The word "אור" can be either a noun (light) or a verb (to give light). Usually, context is enough to disambiguate. Thus in Bereshit 44:3, "הַבֹּקֶר אוֹר" clearly means: "the morning dawned (i.e. became/gave light)" with the word serving as a verb, while "אוֹר גָּדוֹל" in Yeshayahu 9: must mean "the great light", with the word "אור" serving as a noun. However in the phrase "עַד אוֹר הַבֹּקֶר" (Melakhim II 7:9 and elsewhere), the meaning is ambiguous and the words can mean either: "until the morning dawned" or: "until the morning light".¹
בַּחֲלוֹם / בָּאֳנִיָּה – The word בַּחֲלוֹם can mean either "in a boat" or "in the boat". Similarly, בָּאֳנִיָּה (and בׇּאֳנִיּוֹת) can mean either "in the ship/s" or "in a ship / in ships".²